Compression of FASTQ and SAM format sequencing data.

Storage and transmission of the data produced by modern DNA sequencing instruments has become a major concern, which prompted the Pistoia Alliance to pose the SequenceSqueeze contest for compression of FASTQ files. We present several compression entries from the competition, Fastqz and Samcomp/Fqzco...

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Autores principales:	James K Bonfield, Matthew V Mahoney
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/730ede695c1e456db83ad09e7326ce9c
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spelling	oai:doaj.org-article:730ede695c1e456db83ad09e7326ce9c2021-11-18T07:52:19ZCompression of FASTQ and SAM format sequencing data.1932-620310.1371/journal.pone.0059190https://doaj.org/article/730ede695c1e456db83ad09e7326ce9c2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23533605/?tool=EBIhttps://doaj.org/toc/1932-6203Storage and transmission of the data produced by modern DNA sequencing instruments has become a major concern, which prompted the Pistoia Alliance to pose the SequenceSqueeze contest for compression of FASTQ files. We present several compression entries from the competition, Fastqz and Samcomp/Fqzcomp, including the winning entry. These are compared against existing algorithms for both reference based compression (CRAM, Goby) and non-reference based compression (DSRC, BAM) and other recently published competition entries (Quip, SCALCE). The tools are shown to be the new Pareto frontier for FASTQ compression, offering state of the art ratios at affordable CPU costs. All programs are freely available on SourceForge. Fastqz: https://sourceforge.net/projects/fastqz/, fqzcomp: https://sourceforge.net/projects/fqzcomp/, and samcomp: https://sourceforge.net/projects/samcomp/.James K BonfieldMatthew V MahoneyPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 3, p e59190 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q James K Bonfield Matthew V Mahoney Compression of FASTQ and SAM format sequencing data.
description	Storage and transmission of the data produced by modern DNA sequencing instruments has become a major concern, which prompted the Pistoia Alliance to pose the SequenceSqueeze contest for compression of FASTQ files. We present several compression entries from the competition, Fastqz and Samcomp/Fqzcomp, including the winning entry. These are compared against existing algorithms for both reference based compression (CRAM, Goby) and non-reference based compression (DSRC, BAM) and other recently published competition entries (Quip, SCALCE). The tools are shown to be the new Pareto frontier for FASTQ compression, offering state of the art ratios at affordable CPU costs. All programs are freely available on SourceForge. Fastqz: https://sourceforge.net/projects/fastqz/, fqzcomp: https://sourceforge.net/projects/fqzcomp/, and samcomp: https://sourceforge.net/projects/samcomp/.
format	article
author	James K Bonfield Matthew V Mahoney
author_facet	James K Bonfield Matthew V Mahoney
author_sort	James K Bonfield
title	Compression of FASTQ and SAM format sequencing data.
title_short	Compression of FASTQ and SAM format sequencing data.
title_full	Compression of FASTQ and SAM format sequencing data.
title_fullStr	Compression of FASTQ and SAM format sequencing data.
title_full_unstemmed	Compression of FASTQ and SAM format sequencing data.
title_sort	compression of fastq and sam format sequencing data.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/730ede695c1e456db83ad09e7326ce9c
work_keys_str_mv	AT jameskbonfield compressionoffastqandsamformatsequencingdata AT matthewvmahoney compressionoffastqandsamformatsequencingdata
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Compression of FASTQ and SAM format sequencing data.

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